Possibly what he is interested in is a system WITHOUT PBC? I don't think with PBC the system is really "confined", since there is no true wall to reflect the colliding molecules. Thus to study the effect of real confinement, it is necessary to remove PBC and impose reflective boundary conditions. I am only guessing! :)
--Suman. Omer Markovitch wrote: > In short - you can apply PBC in all directions (XYZ) by choosing the > proper keyword in the .mdp file, I believe the box dimensions are > defined in .gro file. > Omer. > > Koby Levy research group, > Weizmann Institute of Science. > http://www.weizmann.ac.il/sb/faculty_pages/Levy/ > > > On Fri, Oct 10, 2008 at 16:00, Lee Soin <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > Maybe I didn't put it clearly. My intention is to simulate a protein > confined in a box, and the problem is that I don't know how to > define a boundary, or a wall, in GROMACS. > > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is > believed to be clean. > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
